:orphan: .. _python_cli: ====================================== pd_parser Command Line Interface (CLI) ====================================== Here we list the pd_parser tools that you can use from the command line. .. contents:: Contents :local: :depth: 1 .. _gen_add_events_to_raw: add_events_to_raw ================= .. rst-class:: callout usage: ``add_events_to_raw raw [-h] [--out_fname OUT_FNAME] [--keep_pd_channels] [-v] [-o]`` positional arguments -------------------- raw The electrophysiology filepath options ------- -h, --help show this help message and exit --out_fname OUT_FNAME The name to save out the new raw file out to --keep_pd_channels Whether to keep the channels with the photodiode data. -v, --verbose Whether to print function progress. -o, --overwrite Pass this flag to overwrite an existing file .. _gen_add_pd_off_events: add_pd_off_events ================= .. rst-class:: callout usage: ``add_pd_off_events raw [-h] [--off_event_name OFF_EVENT_NAME] [--max_len MAX_LEN] [--zscore ZSCORE] [--max_flip_i MAX_FLIP_I] [--baseline BASELINE] [-v] [-o]`` positional arguments -------------------- raw The electrophysiology raw object or filepath options ------- -h, --help show this help message and exit --off_event_name OFF_EVENT_NAME The name of the photodiode event --max_len MAX_LEN The length of the longest photodiode event --zscore ZSCORE The same zscore as used for `parse_pd`. --max_flip_i MAX_FLIP_I The same max_flip_i as used for `parse_pd`. --baseline BASELINE The same baseline as used for `parse_pd`. -v, --verbose Whether to print function progress. -o, --overwrite Pass this flag to overwrite an existing file .. _gen_add_relative_events: add_relative_events =================== .. rst-class:: callout usage: ``add_relative_events raw [-h] [--beh BEH] [--relative_event_keys [RELATIVE_EVENT_KEYS ...]] [--relative_event_names [RELATIVE_EVENT_NAMES ...]] [-v] [-o]`` positional arguments -------------------- raw The electrophysiology raw object or filepath options ------- -h, --help show this help message and exit --beh BEH The behavioral tsv filepath --relative_event_keys [RELATIVE_EVENT_KEYS ...] A behavioral key (column) in the tsv file that has the time relative to the photodiode events on the same trial as in the `beh_key` event. --relative_event_names [RELATIVE_EVENT_NAMES ...] The name of the corresponding `relative_event_keys` events -v, --verbose Whether to print function progress. -o, --overwrite Pass this flag to overwrite an existing file .. _gen_find_pd_params: find_pd_params ============== .. rst-class:: callout usage: ``find_pd_params raw [-h] [--pd_ch_names [PD_CH_NAMES ...]] [-v]`` positional arguments -------------------- raw The electrophysiology raw object or filepath options ------- -h, --help show this help message and exit --pd_ch_names [PD_CH_NAMES ...] The name(s) of the channels with the photodiode data. Can be one channel for common referenced recording or two for a bipolar recording. If not provided, the data will be plotted for the user to pick -v, --verbose Whether to print function progress. .. _gen_parse_audio: parse_audio =========== .. rst-class:: callout usage: ``parse_audio raw [-h] [--audio_event_name AUDIO_EVENT_NAME] [--beh BEH] [--beh_key BEH_KEY] [--audio_ch_names [AUDIO_CH_NAMES ...]] [--exclude_shift EXCLUDE_SHIFT] [--resync RESYNC] [--max_len MAX_LEN] [--zscore ZSCORE] [--add_events] [--recover] [-v] [-o]`` positional arguments -------------------- raw TThe electrophysiology raw object or filepath options ------- -h, --help show this help message and exit --audio_event_name AUDIO_EVENT_NAME The name of the audio event --beh BEH The behavioral dictionary or tsv filepath --beh_key BEH_KEY The name of the behavioral key (column) corresponding to the audio event timing --audio_ch_names [AUDIO_CH_NAMES ...] The name(s) of the channels with the audio data. Note that they will be if thereare two channels they will be bipolar referenced --exclude_shift EXCLUDE_SHIFT How many seconds off to exclude an audio-behavioral event difference --resync RESYNC How large of a difference to use to resynchronize events. See `pd_parser.parse_pd` for more information --max_len MAX_LEN The length of the longest audio event --zscore ZSCORE How many standard deviations larger than the baseline the correlation of the audio is. If None, zscore is found interactively. --add_events Whether to run the parser a second time to add more events from deflections corresponding to multiple events on the same channel --recover Whether to recover corrupted events manually. -v, --verbose Whether to print function progress. -o, --overwrite Pass this flag to overwrite an existing file .. _gen_parse_pd: parse_pd ======== .. rst-class:: callout usage: ``parse_pd raw [-h] [--pd_event_name PD_EVENT_NAME] [--beh BEH] [--beh_key BEH_KEY] [--pd_ch_names [PD_CH_NAMES ...]] [--exclude_shift EXCLUDE_SHIFT] [--resync RESYNC] [--max_len MAX_LEN] [--zscore ZSCORE] [--max_flip_i MAX_FLIP_I] [--baseline BASELINE] [--add_events] [--recover] [-v] [-o]`` positional arguments -------------------- raw The electrophysiology raw object or filepath options ------- -h, --help show this help message and exit --pd_event_name PD_EVENT_NAME The name of the photodiode event --beh BEH The behavioral dictionary or tsv filepath --beh_key BEH_KEY The name of the behavioral key (column) corresponding to the photodiode event timing --pd_ch_names [PD_CH_NAMES ...] The name(s) of the channels with the photodiode data. Can be one channel for common referenced recording or two for a bipolar recording. If not provided, the data will be plotted for the user to pick --exclude_shift EXCLUDE_SHIFT How many seconds off to exclude a photodiode- behavioral event difference --resync RESYNC How large of a difference to use to resynchronize events. This is for when events are off but not by much and so they should be excluded but are still needed to fit an alignment.Increase if the alignment is failing because too many events are being excluded, decrease to speed up execution. --max_len MAX_LEN The length of the longest photodiode event --zscore ZSCORE How many standard deviations larger than the baseline the photodiode event is. Decrease if too many events are being found and increase if too few. Use `find_pd_params` to determine if unsure. --max_flip_i MAX_FLIP_I The maximum number of samples the photodiode event takes to transition. Increase if the transitions are not being found, decrease for fewer false positives. --baseline BASELINE How much relative to the max_lento use to idenify the time before the photodiode event. Probably don't change but increasing will reduce false-positives and decreasing will reduce false-negatives. --add_events Whether to run the parser a second time to add more events from deflections corresponding to multiple events on the same channel --recover Whether to recover corrupted events manually. -v, --verbose Whether to print function progress. -o, --overwrite Pass this flag to overwrite an existing file